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- PDB-7bpu: Structural and mechanistic insights into the biosynthesis of Dige... -

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Basic information

Entry
Database: PDB / ID: 7bpu
TitleStructural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes
ComponentsDigeranylgeranylglyceryl phosphate synthase
KeywordsMEMBRANE PROTEIN / Lipid
Function / homology
Function and homology information


geranylgeranylglycerol-phosphate geranylgeranyltransferase / geranylgeranylglycerol-phosphate geranylgeranyltransferase activity / glycerophospholipid biosynthetic process / magnesium ion binding / plasma membrane
Similarity search - Function
Digeranylgeranylglyceryl phosphate synthase / : / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family
Similarity search - Domain/homology
PHOSPHATE ION / Digeranylgeranylglyceryl phosphate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.32 Å
AuthorsCheng, W. / Ren, S.
CitationJournal: Cell Rep / Year: 2020
Title: Structural and Functional Insights into an Archaeal Lipid Synthase
Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / ...Authors: Ren, S. / de Kok, N.A. / Gu, Y. / Yan, W. / Sun, Q. / Chen, Y. / He, J. / Tian, L. / Andringa, R.L. / Zhu, X. / Tang, M. / Qi, S. / Xu, H. / Ren, H. / Fu, X. / Minnaard, A.J. / Yang, S. / Zhang, W. / Li, W. / Wei, Y. / Driessen, A.J. / Cheng, W.
History
DepositionMar 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Digeranylgeranylglyceryl phosphate synthase
B: Digeranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7614
Polymers63,5712
Non-polymers1902
Water00
1
A: Digeranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8812
Polymers31,7861
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-3 kcal/mol
Surface area14050 Å2
MethodPISA
2
B: Digeranylgeranylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8812
Polymers31,7861
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.360, 134.060, 79.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Digeranylgeranylglyceryl phosphate synthase / DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol- ...DGGGPS / (S)-2 / 3-di-O-geranylgeranylglyceryl phosphate synthase / Geranylgeranylglycerol-phosphate geranylgeranyltransferase


Mass: 31785.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ0279 / Production host: Escherichia coli ATCC 8739 (bacteria)
References: UniProt: Q57727, geranylgeranylglycerol-phosphate geranylgeranyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 200 mM NaCl, 20% (w/v) PEG500, and 200 mM Tris-HCl (pH 8.0).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.32→48.53 Å / Num. obs: 21570 / % possible obs: 99.7 % / Redundancy: 6.732 % / Biso Wilson estimate: 80 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.218 / Χ2: 1.041 / Net I/σ(I): 10.41
Reflection shellResolution: 3.52→3.76 Å / Redundancy: 6.803 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.91 / Num. unique obs: 3248 / CC1/2: 0.977 / Rrim(I) all: 0.507 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575:???refinement
HKL-2000v1.0data reduction
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 3.32→48.53 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.557
RfactorNum. reflection% reflectionSelection details
Rfree0.277 584 5.01 %RANDOM
Rwork0.246 ---
obs0.247 11662 99.7 %-
Displacement parametersBiso max: 140.23 Å2 / Biso mean: 62.67 Å2 / Biso min: 37.53 Å2
Baniso -1Baniso -2Baniso -3
1-10.2031 Å20 Å20 Å2
2---17.421 Å20 Å2
3---7.2179 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: final / Resolution: 3.32→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 10 0 4436
Biso mean--116.22 --
Num. residues----558
LS refinement shellResolution: 3.32→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.2463 21 5.21 %
Rwork0.2455 382 -
all0.2456 403 -
obs--93.91 %

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